Overuse of inorganic fertilizers have contributed to an increase in soil acidity in global arable land and consequently caused an increase in Aluminium ion (Al3+) toxicity and a reduction of crop yield of between 30-50% in developing countries. Studies show that Al3+ toxicity inhibits cell division in the root tip meristem in sensitive plants even at micromolar concentrations. Applications of lime, manure and compost are some of the most common methods used to overcome the impact of Al3+ toxicity. Other studies have identified natural variation for the multigenic Al3+ tolerance trait in many crop species and can be utilized in crop improvement. This review highlights a search for a clearer understanding of the molecular basis for Aluminium ion toxicity by correlating heterosis and epigenetic mechanisms like DNA Cytosine methylation in inbred and reciprocal maize hybrids crosses. Several recent studies indicated that the global differential gene expression regulated by epigenetic mechanisms between hybrids and parental inbred lines can potentially contribute to heterosis in maize.